annotations in biomedicine & ongoing work of the w3c open annotation community group
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2012 CNI Fall Membership Meeting, Dec 10 th 2012, Washington DC. Annotations in Biomedicine & Ongoing Work of the W3C Open Annotation Community Group. Paolo Ciccarese, PhD. [email protected]. Mass General Hospital. Harvard Medical School. Annotation in Biomedicine. - PowerPoint PPT PresentationTRANSCRIPT
Annotations in Biomedicine & Ongoing Work of the W3C Open Annotation Community Group
Paolo Ciccarese, PhD
Mass General Hospital Harvard Medical School
2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC
Annotation in Biomedicine
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
As (biomedical) scientists…
• We deal with an increasing amount of digital resources: documents, images, videos, datasets, vocabularies, databases, software…– About 150-200 articles a week– 10mins/article ≈ 34 hours/week– How can we manage it?
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Limitations of the Web of Documents
• Machines don’t do very well in *understanding* documents and have difficulties to find, present, access, or maintain available electronic information on the web
• Need for a data representation to enable software products (agents) to provide access to heterogeneous and distributed information– Tasks often require to combine data on the Web– Humans combine these information easily** even if different
terminologies are used and the information is incomplete, or buried in images and videos
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Semantic tagging
APP
News and Hypotheses
Biol
ogic
al P
roce
sses
Videos/imagesPathways Expe
rts
Antibodies 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Document Metadata Exchange Organizer
• Domeo is a web application for producing and sharing manual and semi-automatic (structured/unstructured) stand-off annotation
• Domeo is designed as an open system
Ciccarese et al, 2012Open semantic annotation of scientific publications using DOMEO http://www.jbiomedsem.com/content/3/S1/S1
http://annotationframework.org
https://twitter.com/DomeoTool
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Semantic tagging through ontologies
http://purl.obolibrary.org/obo/PR_000004168Label ‘amyloid beta A4 protein’Exact synonyms ‘APP’, ‘amyloidogenic glycoprotein’, …Related Synonyms ‘A4’, ‘ABPP’,
Is a http://purl.obolibrary.org/obo/PR_000000001Label ‘protein’Definition ‘An amino acid chain that…’
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
APPs
for t
he S
eman
tic R
esou
rces
Pro
ject
, May
201
0
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Reagents (reproducibility)
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
antibodyregistry.org
Annotation of Argumentation
classic publication
scientific discourse ‘semantic’ representation
http://tinyurl.com/cgyna2m
Semantic Web Applications in Neuromedicine (SWAN) project [2007]
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
graph representation
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Drupal Framework for building online scientific communitieshttp://sciencecollaboration.org/
Dynamic inventory of Web-based neuroscience resourceshttp://www.neuinfo.org/
Viz. ann. systems
Analysis
Annotation Sharing
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Video AnnotationTools
Annotation Ontology (AO)
• OWL vocabulary for representing and sharing annotation of digital resources and their fragments in RDF format
• Focus on biomedicine and sciences. But desire to make the AO framework more broadly usable.
Ciccarese et al, 2011An open annotation ontology for science on web 3.0http://www.jbiomedsem.com/content/2/S2/S4
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Annotation Ontology Network
The Living DocumentProject
Biotea
Annotations at Harvard
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Open Annotation Collaboration
• Focus on interoperability for annotations in order to allow sharing of annotations across:– Annotation clients;– Content collections;– Services that leverage annotations.
• Focus on annotation for scholarly purposes. But desire to make the OAC framework more broadly usable.
http://openannotation.org/ 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Take Note Site Visit, November 1st 2012
AO+OAC = W3C Open Annotation
• Annotation Ontology and Open Annotation Collaboration have been merged to create the W3C Open Annotation Community Group
• Officially started in February 2012
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
W3C Open Annotation Community Group
• Is working towards a common, RDF-based, specification for annotating digital resources:– Aligned with WWW Architecture & Linked Open Data
best practices– Focus on interoperability – the sharing of
annotations across clients, servers, repositories and applications
– Annotations are treated as first class Web resources, i.e., referenceable and available to themselves be annotated
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
http://www.w3.org/community/openannotation/
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Participants
54 ParticipantsFrom more than 30 institutionsAdditional users interact through the mailing list
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Public Mailing List
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Specifications (Drafts)
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Plans for Open Annotation 1.0 Release
• Currently working on a new draft and a new tutorial that will be published in mid January for collecting further feedback
• We are planning a release of Open Annotation Model v. 1.0 for March/April
• They will have a new structure that we believe will help lowering the learning and implementation curves
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Acknowledgements
• Tim Clark, Director of MIND Informatics• Domeo Support: Maryann Martone, Anita
Bandrowski, Vadim Astakhov, Anita de Waard, Bradley Allen, Keith Gutfreund, Antony Scerri
• W3C Community Group: Robert Sanderson, Herbert van de Sompel and all the members
• Funding: National Institutes of Health, Elsevier Laboratories, and Eli Lilly & Co.
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD